Contacts of the helix formed by residues 10 - 27 (chain B) in PDB entry 1QRV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B PRO 3.4 4.9 + - - -
9B LEU* 1.3 76.5 - - - +
11B ALA* 1.3 58.5 + - - +
12B TYR* 3.3 13.4 + - - +
13B MET* 2.8 29.2 + - - +
14B LEU* 2.8 28.6 + - - +
56B ALA* 4.0 2.0 - - - -
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER* 1.3 73.8 - - - +
12B TYR* 1.3 64.4 + - - +
14B LEU* 3.7 2.6 - - - +
15B TRP 3.1 17.3 + - - -
43B TRP* 3.4 20.6 - - + -
52B TRP* 3.3 34.0 - - - +
53B GLU* 3.9 12.3 - - + +
56B ALA* 3.4 19.5 - - + +
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Residues in contact with TYR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER* 3.1 10.4 - - - +
11B ALA* 1.3 79.5 - - - +
13B MET* 1.3 72.4 + - + +
15B TRP* 3.2 25.2 + + - +
16B LEU* 2.9 50.0 + - + +
36B ALA* 3.7 23.0 + - - +
39B GLY* 4.1 5.1 - - - -
40B GLY* 4.2 5.2 + - - -
43B TRP* 3.6 51.2 - + + +
20D C 5.3 1.8 + - - -
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Residues in contact with MET 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.6 27.8 - - + -
10B SER* 2.8 24.6 + - - +
12B TYR* 1.3 84.9 - - + +
14B LEU* 1.3 66.6 + - - +
16B LEU* 3.8 26.9 - - + -
17B ASN* 3.0 28.2 + - - +
20B ARG* 4.1 2.0 - - - -
1C G 3.7 13.0 - - + +
20D C 3.8 45.5 - - + +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.7 33.8 - - + +
10B SER 2.8 26.4 + - - +
11B ALA* 3.7 4.3 - - - +
13B MET* 1.3 74.6 - - - +
15B TRP* 1.3 65.7 + - - +
17B ASN* 3.5 8.2 + - - +
18B SER* 3.4 12.1 + - - -
52B TRP* 3.8 21.4 - - + +
55B LYS* 3.6 18.4 - - + +
56B ALA* 3.2 42.4 - - + +
59B ALA* 4.8 4.9 - - + -
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Residues in contact with TRP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA 3.1 3.4 + - - +
12B TYR* 3.5 22.7 - + - +
14B LEU* 1.3 79.9 - - - +
16B LEU* 1.3 75.0 + - + +
18B SER* 2.6 25.2 + - - -
19B ALA* 2.7 41.1 + - + +
23B ILE* 4.3 5.2 - - + -
39B GLY* 2.9 46.2 - - - -
42B LEU* 3.6 26.7 - - + -
43B TRP* 3.5 35.9 - + + -
46B MET* 3.6 15.0 - - + +
52B TRP* 3.5 41.4 - + + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 2.9 43.2 + - + +
13B MET* 3.8 27.8 - - + +
15B TRP* 1.3 90.5 - - + +
17B ASN* 1.3 58.0 + - - +
19B ALA* 4.2 1.3 - - - +
20B ARG* 2.7 48.9 + - - +
23B ILE* 4.1 25.4 - - + -
35B VAL* 4.4 15.0 - - + +
36B ALA* 5.4 5.2 - - - -
39B GLY* 4.4 5.2 - - - -
20D C 4.2 11.2 - - - +
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Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.1 15.0 - - - +
13B MET* 3.0 23.9 + - - +
14B LEU* 3.7 6.7 - - - +
16B LEU* 1.3 76.1 - - - +
18B SER* 1.3 62.9 + - - +
20B ARG* 2.6 49.7 + - - +
21B GLU 5.0 0.7 + - - -
1C G 2.8 39.6 + - - +
2C C 3.7 22.7 + - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 3.4 4.6 + - - -
15B TRP* 2.6 22.9 + - - -
17B ASN* 1.3 77.8 - - - +
19B ALA* 1.3 58.4 + - - +
20B ARG 3.6 0.2 - - - -
21B GLU* 5.0 2.8 + - - +
22B SER* 5.4 2.1 + - - -
52B TRP* 3.0 35.4 - - - -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 2.7 52.9 + - + +
16B LEU* 3.0 3.8 + - - +
18B SER* 1.3 75.3 - - - +
20B ARG* 1.3 56.8 + - - +
21B GLU 3.4 3.1 - - - -
22B SER* 3.3 13.6 + - - -
23B ILE* 3.0 34.1 + - + +
42B LEU* 6.1 0.2 - - + -
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B MET* 4.1 7.5 - - - -
16B LEU* 2.7 32.4 + - + +
17B ASN* 2.6 54.3 + - - +
18B SER 3.6 1.6 - - - -
19B ALA* 1.3 69.7 - - - +
21B GLU* 1.3 67.4 + - + +
23B ILE* 3.5 5.3 + - - +
24B LYS* 3.1 52.1 + - + +
35B VAL* 4.4 17.5 - - + +
1C G 4.2 3.4 - - - +
2C C 4.2 23.6 + - - -
3C G 4.6 14.3 + - - -
20D C 4.7 3.0 + - - -
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASN 5.0 1.2 + - - -
18B SER 5.0 2.6 + - - +
19B ALA 3.4 0.6 - - - -
20B ARG* 1.3 76.2 - - - +
22B SER* 1.3 52.9 + - - +
24B LYS* 3.0 17.4 + - - +
25B ARG* 2.7 36.4 + - - +
3C G 5.7 4.7 - - - +
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER 5.4 1.3 + - - -
19B ALA* 3.3 18.0 + - - -
21B GLU* 1.3 79.0 - - - +
23B ILE* 1.3 63.3 + - - +
25B ARG* 3.1 9.8 + - - +
26B GLU* 3.1 40.3 + - - +
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 4.3 4.9 - - + -
16B LEU* 4.1 16.2 - - + -
19B ALA* 3.0 21.8 + - + +
20B ARG* 3.9 4.9 - - - +
21B GLU 3.3 0.2 - - - -
22B SER* 1.3 77.6 - - - +
24B LYS* 1.3 58.9 + - - +
26B GLU* 3.4 4.7 + - - -
27B ASN* 2.7 51.4 + - - +
30B ILE* 4.2 1.6 - - + -
35B VAL* 4.0 25.8 - - + +
38B ARG* 4.0 12.8 - - + -
39B GLY* 3.4 34.5 - - - +
42B LEU* 3.8 23.6 - - + -
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 3.1 42.5 + - + +
21B GLU* 3.0 15.8 + - - +
23B ILE* 1.3 76.1 - - - +
25B ARG* 1.3 66.2 + - - +
27B ASN 3.3 15.9 - - - +
28B PRO* 3.6 5.4 - - - +
29B GLY 5.1 0.2 + - - -
30B ILE* 4.0 25.8 - - + +
35B VAL* 4.0 13.5 - - + -
3C G 4.8 10.5 - - - -
4C A 4.5 16.8 + - - -
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU 2.7 16.5 + - - +
22B SER* 3.1 11.6 + - - +
24B LYS* 1.3 76.5 - - - +
26B GLU* 1.3 84.7 + - - +
27B ASN 3.3 0.7 + - - -
28B PRO* 3.7 15.1 - - - +
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER* 3.1 30.8 + - - +
23B ILE* 4.0 8.2 - - - +
24B LYS 3.3 0.2 - - - -
25B ARG* 1.3 94.0 + - - +
27B ASN* 1.3 69.6 + - - +
28B PRO* 3.6 7.1 - - - +
38B ARG* 5.2 6.6 + - - +
42B LEU* 4.8 12.8 - - - +
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 2.7 42.4 + - - +
24B LYS 3.3 4.6 - - - +
25B ARG 3.2 0.2 - - - -
26B GLU* 1.3 90.6 + - - +
28B PRO* 1.3 69.9 - - - +
29B GLY 3.4 0.2 + - - -
30B ILE* 2.9 43.9 + - + +
38B ARG* 3.7 25.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il